On 11/2/13 6:50 PM, Xu Dong Huang wrote:
@ Gromacs users,
so I did g_dist , and I’m confused by a couple of things. 1) why is it asking
me for 2 groups? I have my particles of interest under 1 type, namely [ O1 ] 1
2 3, and nothing else. 2) I just picked the same group twice, and the
result is gives me in xvg is the following
There are no distances measured, that cannot be right.
You can't just hope for magic. Please read g_dist -h to understand what the
program is doing. Like I said, you have to measure each distance manually, i.e.
individually. You need three index groups:
[ 1 ]
1
[ 2 ]
2
[ 3 ]
3
Then measure the distances between 1&2, 2&3, and 1&3. Post-process each
individually to get the distributions or pool the data (cat the resulting files)
and get the distribution from that, if it is in any way meaningful.
0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
20.0000000 0.0000000 0.0000000 0.0000000 0.0000000
40.0000000 0.0000000 0.0000000 0.0000000 0.0000000
60.0000000 0.0000000 0.0000000 0.0000000 0.0000000
80.0000000 0.0000000 0.0000000 0.0000000 0.0000000
100.0000000 0.0000000 0.0000000 0.0000000 0.0000000
120.0000000 0.0000000 0.0000000 0.0000000 0.0000000
140.0000000 0.0000000 0.0000000 0.0000000 0.0000000
160.0000000 0.0000000 0.0000000 0.0000000 0.0000000
180.0000000 0.0000000 0.0000000 0.0000000 0.0000000
200.0000000 0.0000000 0.0000000 0.0000000 0.0000000
220.0000000 0.0000000 0.0000000 0.0000000 0.0000000
240.0000000 0.0000000 0.0000000 0.0000000 0.0000000
260.0000000 0.0000000 0.0000000 0.0000000 0.0000000
…
Makes sense; the distance between any one group and itself is zero.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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